madhu biyani - biyani bio solutionsbiyanibiosolutions.com/cv_madhu_biyani.pdf · [6] madhu biyani,...

Curriculum Vitae Madhu Biyani (2014)

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Madhu Biyani

Physician (India), Ph.D. (Japan)

[Nationality: Citizen of India and Permanent Residence of Japan]

Academic career:

B.H.M.S. (Doctor in Bachelor of Homoeopathy Medicine and Surgery) from University of Rajasthan, INDIA (July 2000). [enclosure: p12]

Ph.D. (Doctor of Engineering) in Bioengineering from Saitama University, JAPAN (March 2011).

Title: Development of a general method to create a protease activity-enhancing peptide aptamers for drug discovery. [enclosure: p13-14]

Japanese-Language Proficiency Test-N3 Level [enclosure: p15-16]

Research and Professional Career:

01/2006 - 09/2007: Researcher in REDS Group (Rational Evolutionary Design of Advanced Biomolécules, Saitama), CREATE (JST), Japan [enclosure: p17]

04/2009 - 03/2013: Research associate in City Area Project (JST), Saitama University, Japan [enclosure: p18]

12/2012 - 3/2014: Research associate in Sentan Project (JST), Saitama University, Japan [enclosure: p19-20]

4/2014 – 9/2014: Post doc researcher in CoI project, Kaneko lab, School of Materials Science, JAIST, Japan [enclosure: p21]

Contacts:

Present Residence: E42, Asahidai 1-50, Nomi, Ishikawa 923-1211, Japan

Permanent Residence in Japan: 1042-8, Shimo-okubo, Sakura-ku, Saitama 338-0825

Permanent Residence in India: C1-C2, L.S. Nagar, Sector-3, Vidhyadhar Nagar,

Jaipur 302023

Email: [email protected]; [email protected]; 080-9191-9989 (mobile)


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List of Publications

Patent:

[1] Koichi Nishigaki, Koichiro Kitamura, Madhu Biyani, Masae Futakami, Kenji

Yamamoto, Tomoyo Kawakubo. Peptide selected (Materials patent), Patent

Application No.: 2009-245763, filing date: October 26, 2009.

Journal Papers (International):

[1] Madhu Biyani, Masae Futakami, Koichiro Kitamura, Miho Suzuki, Tomoyo

Kawakubo, Kenji Yamamoto and Koichi Nishigaki. In vitro selection of cathepsin

E-activity-enhancing peptide aptamers at neutral pH. International Journal of

Peptides (2011) doi:10.1155/2011/834525.

[2] Koichiro Kitamura, Madhu Biyani, Masae Futakami, Miho Suzuki, Tomoyo

Kawakubo, Kenji Yamamoto and Koichi Nishigaki. Peptide aptamer-based

ELISA-like system for detection of cathepsin E in tissues and plasma. J Mol

Biomark Diagn. (2011), 2:104. doi:10.4172/2155-9929.1000104.

[3] Manish Biyani, Madhu Biyani, Naoto Nemoto, Takanori Ichiki, Koichi Nishigaki,

Yuzuru Husimi. Gel-shift selection of translation enhancer sequences using

mRNA display. Analytical Biochemistry, (2011) Feb 1; 409(1):105-11.

[4] Koichiro Kitamura, Masayuki Komatsu, Madhu Biyani, Tomovo Kawakubo, Kenji

Yamamoto, and Koichi Nishigaki. Proven in vitro evolution of protease

cathespsin E- inhibitors and activators at pH 4.5 using a paired peptide method. J

Pept Sci. (2012) Oct 30. doi : 10. 1002/psc.2453.

[5] Masayuki Komatsu, Madhu Biyani, Sunita Ghimire Gautam and Koichi Nishigaki.

Peptide-modulated activity enhancement of acidic protease cathepsin E at neutral

pH. International Journal of peptide (2012) 2012, Article ID 316432.

[6] Koichiro Kitamura, Madhu Biyani, Taku Ozawa, Miho Suzuki, Naoto Nemoto, and

Koichi Nishigaki. Alpha-strand peptide scaffold: a novel and simple peptide

conjugating approach for improving the function of peptide in pep-ELISA. J Mol

Biomark Diagn. (under communication)


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[7] Madhu Biyani, Sunita Ghimire Gautam, Masayuki Komatsu, Sachika Tsuji-Ueno,

Manish Biyani and Koichi Nishigaki. Proven evolution of proteins: Progressive

Library Method in in-vitro evolution. Brief. Funct. Genomics (to be submitted).

Journal Papers (National):

[8] Takuyo Aita, Yasunori Kinoshita, Masae Futakami, Md. Salimullah, Madhu Biyani,

Sachika Tsuji, Masaki Shibuya, Osamu Takei, Koichiro Kitamura, Naoto Nemoto,

and Koichi Nishigaki. Report of Comprehensive Open Innovation Center,

Saitama University (2008).

[9] Koichi Nishigaki, Takafumi Sakai, Naoto Nemoto, Akihito Adachi, Hidekazu

Uchida, Yuki Hasegawa, Takuyo Aita, Shingo Ueno, Masae Futakami, Koichiro

Kitamura, Madhu Biyani, Kenji Yamamoto, Tomoyo Kawakubo, Atsushi Agouchi,

Kenji Sakimura, Manabu Abe, Yuko Hotta, Hitoshi Goto, Mikio Tomida, Tatsuya

Tominaga, Hideo Nakajima, Kenjyu Miura, Tomojirou Hayashi, Shigenari

Kukizaki, Masaki Shibuya, Osamu Takei, Kiyoshi Takayama, Satomi Takizawa,

Takizawa, Takuto Ose, Report of Comprehensive Open Innovation Center,

Saitama University (2009).

Book chapters:

[10] Manish Biyani, Madhu Biyani, Naoto Nemoto, Yuzuru Husimi. Evolutionary

molecular engineering to efficiently direct in vitro protein sysnthesis. In: Protein

Synthesis, ISBN-980-953-307-170-6, InTech Publisher, Croatia (2012).

[11] Madhu Biyani, Koichi Nishigaki, and Manish Biyani. Biomolecular Display

Technologies for Biomedical Research and Drug Discovery. In: Animal

Biotechnology. Elsevier Publisher (to be appeared in July 2013).

Conferences Papers (International):

[1] Madhu Biyani, Koichi Nishigaki. Peptide-aptamer -based drug development for

cancer. BICON 2012, Drug-development: a Collaborative Approach of

Chemist and Biologist (September 2012) (Oral)


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[2] Madhu Biyani, Koichiro Kitamura, Koichi Nishigaki. Peptide-based ELISA-like

system for cancer diagnosis. BICON 2011, Innovation in the Latest Healthcare

Issues (September 2011) (Oral)

[3] Madhu Biyani, Masae Futakami, Koichiro kitamura, Tomoyo Kawakubo, Miho

Suzuki, Kenji Yamamoto, Koichi Nishigaki. Screening of protease-activating

peptide aptamers at neutral pH aiming for the cancer therapeutics (BMB 2010,

Dec.7-10 Kobe) (Poster)

[4] Madhu Biyani, Koichi Nishigaki. Protease-activating peptide aptamers: a novel

approach for the bio drug discovery aimed for cancer. 5th Indo-Japan Conference

on Innovative Molecular Approaches in Global Health Research (September,

2010) (Oral)

[5] Koichi Nishigaki, Koichiro Kitamura, Chuya Yoshida, Masae Futakami, Madhu

Biyani, Sachika Ueno-Tsuji. Strategy and technology for the evolution of novel

proteins: Progressive Library Method (Bio-Physical Society of Japan 2010, Sept,

Sendai) (Poster)

[6] Madhu Biyani, Masae Futakami, Koichiro Kitamura, Koichi Nishigaki. Selection of

cathepsin E-activating peptides at neutral pH using a Progressive Library Method

(Molecular Biology Society of Japan 2009, Dec 9-12,Yokohama) (Poster)

[7] Masae Futakami, Madhu Biyani, Koichiro Kitamura, Koichi Nishigaki. Paired

peptide method effective for advancing cathepsin E-activating activities of peptides

(Molecular Biology Society of Japan 2009, Dec 9-12, Yokohama) (Poster)

[8] Koichiro Kitamura, Madhu Biyani, Masae Futakami, Tomoyo Kawakubo, Kenji

Yamamoto, Koichi Nishigaki. Application of cathepsin-E specific binding peptides

for a diagnostic reagent kit (Molecular Biology Society of Japan 2009, Dec 9-12,

Yokohama) (Poster)

[9] Madhu Biyani and Koichi Nishigaki. Peptide technology for next generation

targeted biotherapeutics. 4th Indo-Japan Conference on Nanotechnology and

Healthcare in the Developing world (September, 2009) (Oral)

[10] 西垣功一、幸一郎、木保則、田昼也、ハ・サ、辻

幸香、野真吾、マ・ビー、二恵、高橋陽子、マ

・ビー、澁谷昌樹、武居修、浅見太、鈴木美穂、根本直人、

ハ・ン、二木類、相田拓洋、内田秀和、後藤仁志、山本健


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二、草木稔篤、花田和則、大関正弘、伏見譲 , 高速分子技術

eRAPANSY：未来型創薬ー . (BMB 2008, Dec. 9-12 Kobe) (Poster).

[11] Madhu Biyani and Koichi Nishigaki. Peptide Pairs: a novel approach for directed

evolution of Cathepsin-E inhibitor/activator. 3rd Indo-Japan Conference on

Facilitating interdisciplinary biotech for future entrepreneurship (August,

2008) (Oral)

[12] Madhu Biyani and Koichi Nishigaki. Synergy of Evolutionary Biology and future of

Biotech in Medicine. 2nd Indo-Japan Conference on Research-based

Education (June, 2007) (Oral)

[13] Madhu Biyani and Koichi Nishigaki. Evolutionary Biotechnologies: Understanding

the origin of life for future biotech. 1st Indo-Japan Conference on Research-

based Education (June, 2006) (Oral)

[14] Madhu Biyani and Koichi Nishgiaki. Control of cell-free translation initiation by

evolving a universal regulatory sequence using genotype-phenotype linking

technology. International Conference in Bio-Physics, Kyoto, Japan (July, 2006)

(Poster).

Conferences papers (National):

[15] Madhu Biyani, Koichiro Kitamura, Masae Futakami, Tomoyo Kawakubo, Kenji

Yamamoto, Koichi Nishigaki. 15th Japan Society for Proteases in

Pathophysiology (CPIPT 2010, August 21-21,Osaka) (Oral & Poster)

[16] Koichiro Kitamura, Madhu Biyani, Masae Futakami, Tomoyo Kawakubo, Kenji

Yamamoto, Koichi Nishigaki. 14th Japan Society for Proteases in

Pathophysiology (CPIPT 2009, August 21-22,Osaka) (Oral & Poster)


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Awards and Achievements

[1] Obtained national scholarship from Government of India for getting first rank

in Secondary Board Examinations.

[2] Obtained Shri T.W. Lala Smarati Prize for getting higher marks in Senior

Higher Secondary Examinations.

[3] Obtained outstanding academic award certificate and cash prize from

Homeopathic medical association of India, Ajmer Unit.

[4] Obtained appreciation letter from Tigers Welfare society for participation in

social activities.

[5] Obtained appreciation letter from Government of Rajasthan, paryavaran

Department for participation in essay writing competition.

[6] Obtained Certificate for Participation in National Homeopathic Conference

held in Jaipur.

[7] Obtained 3rd rank in Japanese language contest in Saitama organized by

WFWP program.

[8] Obtained Prize for High School lecture about Indian culture in Saitama.


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Brief description of previous researches

The most important Scientific achievements from my past research are based on my

great interest as a being researcher and physician to discover the therapeutic

biomolecules such as highly functional peptide aptamers for the most incurable

diseases such as cancer by mainly advancing the in vitro evolution method. These are

grouped in major three projects and are briefly described below:

I. Development of progressive library method and its application to

generation of peptide-aptamer-based inhibitors and activators of

Cathepsin E.

Molecules of high activity (affinity) are essential tools for both diagnostics

and target therapeutics. However, to identify such molecules ab initio is not

so difficult than to further improve their particular function. Here, we

developed a selection method, called ‘progressive library method (PLM)’ to

acquire highly affinity and functional peptides. This is an advanced, systemic

in vitro evolution, and integrated method that equipped with three successive

library constructions and selections that offers advantages for the

construction of succeeding libraries based on the previous library selection

information and for the enrichment of molecules based on high activity (e.g.,

enzyme-inhibition and -activation) and not merely binding affinity. Herein,

the primary library selection provides the search of particular functional

peptides (inhibitors, activators, or binders) from the huge random peptides

library and enriches the library with peptides of marginal range of affinities

and functions. The selected peptides from primary library are divided into

blocks of 4 amino acids and recombined again by block shuffling method for

preparing the secondary library for next round selection. Finally, the selected

peptides from secondary library were further converted to randomly generate

paired peptides library that plays the most critical role to further elevate the

affinity and function of the peptides at the highest level. Herein, the primary,

secondary, and tertiary library selections can be regarded as module-finding,

module-shuffling and module pairing, respectively, which closely resembles

the progression of the natural evolution of proteins. Thus, PLM represents

an effective approach to assist evolutionary protein engineering to meet the

demands of modern drug discovery as well in harmony of protein science.


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Achievements:

1) A ‘Progressive Library Method’ is successfully developed and applied to

select peptide aptamer against cathepsin E (CE), an aspartic protease that

has been associated to induce apoptosis in cancer cells. CE-activator

peptides were obtained at acidic pH with the ultra-high affinity (100 pM

dissociation constant) and the highest CE activity (47.8%).

2) This is the first time that the activity enhancing binding peptides were

selected successfully at neutral pH with the highest affinities (peptide of

300 nM KD, selected from the secondary library and peptide of improved

2 nM KD, selected from the third library) against CE. The presence of

these peptides in apoptosis induction in vivo assay which increased the

enhancing of CE-activity and induced cell apoptosis indicates their

potential to act as cancer drug precursors.

3) This work resulted one patent and three journal articles (Int. J. Pept.,

2011; Int. J. Pept., 2012; J. Pept. Sci., 2012). The work was also presented as

talks and posters in 9 national and international meetings. This work also

brought the winning award for the best young investigator in 17th Japan

Society of Pathology of Protease (CPIPT, 2012).

Recently, PLM was demonstrated successfully by other researchers to

acquire the novel higher affinities peptide aptamers against various

therapeutic targets including Aβ42 oligomers (for Alzheimer’s disease)

(Protein Pept. Lett., 2011), NM23 (for Cancer) and SOD1 (for Motor neuron

disease).

II. Development of Peptide aptamer-based ELISA-like system for

detection of cathepsin E in tissue and plasma.

ELISA (enzyme-linked immunosorbent assay) is a highly sensitive and

powerful molecular detection tool which is based on antibodies. However,

antibodies are associated with several drawbacks such as their high cost

production and large size. In this study, we reported two types of peptide-

based ELISA-like systems (pep-ELISA). One is enzyme-on-peptide,

which is much simpler as it consists of a peptide and a target enzyme only.

The other mimics the conventional sandwich ELISA where antibodies are

replaced with peptides. These constructs were confirmed to be effective


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using the tissues and blood specimens extracted from CE-wild type and

knockout rats.

Achievements:

1) A novel peptide aptamer-based technology, ‘pep-ELISA’ (as a promising

substitution for antibodies-based method), was developed and

demonstrated successfully with sufficient sensitivity (10 g/ml) for the

detection of CE in tissues and plasma.

2) This work resulted in one journal article (Mol. Biomarkers Diagnosis, 2011)

and talks in 2 national and international meetings.

III. In vitro selection of new regulatory sequence for efficient initiation

of cell-free protein synthesis.

In this work, we developed a new approach for selection of translation

enhancer sequences that enables efficient protein synthesis in cell-free

systems. The selection is based on a gel shift assay of a messenger RNA

(mRNA)-protein fusion product that is synthesized in a cell-free

translation system using an mRNA display method.

Achievements:

1) An efficient translation enhancer sequence capable of more rapid initiation of cell-free protein synthesis, with a minimal translation time of 5 min, than a natural longer enhancer sequence (β-globin) was successfully selected using rabbit translation system. This work resulted in one journal article (Anal-Biochem 2011) and honored by Elsevier Publication as one of the key scientific finding

and highlighted on the Front cover page of Analytical Biochemistry

Journal (issue 209, 2011). The work was awarded by JB OUP prize with exceptional value from IUBMB International Union of Biochemistry and Molecular Biology Society in 2006.


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Experimental Exposure

The following list shows some of the experimental techniques and procedures with

which I am familiar and used in my research work.

Protein purification, protein-immobilization by amine coupling method

In vitro display technology e.g. mRNA /cDNA display

Kd measurement using Biacore SPR method

Polymerase Chain Reaction

Transcription, In vitro protein translation, Reverse transcription

DNA/RNA manipulation (isolation, purification, precipitation).

Agarose gel electrophoresis, SDS-PAGE

Enzyme activity assay

Enzyme Kinetics, Restriction digestion and molecular biology techniques.

Fluorescence microscopy imaging.

BrdU labeling, sectioning and cresyl violet and other staining related to

immunohistochemical studies.

Cloning, sequencing.

Micro gel electrophoresis, Micro temperature gel gradient electrophoresis

NMR and FTIR spectroscopy

NCA synthesis using triphosgene

Polypeptide synthesis by NCA ring opening polymerization (ROP) method using

trans transition metal initiators.

Polypeptide synthesis characterization by NMR, IR, MS, GPC, TGA, CD

Glove-box

Thiol-ene photo addition click chemistry

Organic compounds purification

Protection of amino group of amino acid by CBZ and alloc protection groups.

Film casting of synthesized polypeptide.


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Names and contact addresses of references

Name: Koichi NISHIGAKI

Affiliation: Professor, Saitama University, Japan

Email: [email protected]; Phone: 048-858-3100

Name: Yuzuru HUSHIMI

Affiliation: Professor in President Office, Graduate University of Advanced

Studies (SOKENDAI), Japan

E-mail: [email protected]; Phone: 0468-58-1592

Name: Tatsuo KANEKO

Affiliation: Associate Professor, School of Material Science, JAIST, Japan.

E-mail: [email protected]; Phone: 0761-51-1631


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成 26 2 28 日

研究員・産学官連携研究員・ＶＬ研究員・教務補佐員・博士課程研究員採用予

定者調書

研究代表者の所属

職名・氏名所属マテアサエン研究科

職名准教授氏名山口政之

研究課題等名革新料による次世代ンフテの構築

研究課題等名英語表

注

Construction of Next-generation Infrastructure Systems by InnovativeMaterials

研

究

支

援

者

配属先マテアサエン研究科

フガ

氏名

マビ

Madhu Biyani 女

生日昭和 49 7 8 日

研究支援者が

学生の場研究科・課程研究科課程学

雇用期間成 26 4 1 日～成 27 9 30 日

勤務態様

勤務日曜日～金曜日その

他

勤務時間：～：休憩時間 12：00～13：

00

時間分勤務

経費産学連携等研究費受：・Ｏ・マテ：山口教授

再採用の予定

連絡先電話－－

E-mail [email protected]

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